I see this type of thing happen all the time in pharmaceutical research. I always wondered why some PhDs don't fire on all cylinders. I think it's because in many universities our scientific educations are so specialized and spoon-fed, there's no time for independent thinking and growth.
Yep. I'm a chemist, and speaking from personal experience and observation: the PhD process seriously damages almost everyone who goes through it. Fortunately my self-taught outside interests (other fields of science, and nonscientific subjects) preserved my intellect from being totally destroyed by graduate school.